ample.util.maxcluster module¶

class Maxcluster(maxcluster_exe)[source]¶

Bases: object

# Extract the first chain from the nativePdb

# Create a residueSequenceMap and see if the residues match

# If not use keep_matching to create a nativePdb that has the correct residue sequence`

# Run Maxcluster to compare the models to the native

Methods

prepareNative([nativePdbInfo, resSeqMap])

do stuff

compareDirectory
compareModelList
compareSingle
maxsubSorted
parseLogDirectory
parseLogSingleRmsd
parseLogSingleTm
rmsd
runCompareDirectory
run_compare_model_list
tm
tmSorted

compareDirectory(nativePdbInfo=None, resSeqMap=None, modelsDirectory=None, workdir=None)[source]¶

compareModelList(nativePdbInfo=None, resSeqMap=None, models=None, workdir=None)[source]¶

compareSingle(nativePdb=None, modelPdb=None, sequenceIndependant=True, rmsd=False, workdir=None)[source]¶

maxsubSorted(reverse=True)[source]¶

parseLogDirectory(logfile=None)[source]¶

parseLogSingleRmsd(logfile=None)[source]¶

parseLogSingleTm(logfile=None)[source]¶

prepareNative(nativePdbInfo=None, resSeqMap=None)[source]¶

do stuff

rmsd(model)[source]¶

runCompareDirectory(nativePdb=None, modelsDirectory=None, logfile=None)[source]¶

run_compare_model_list(nativePdb=None, models=None, logfile=None)[source]¶

tm(model)[source]¶

tmSorted(reverse=True)[source]¶

find_maxcluster(amoptd)[source]¶

Return path to maxcluster binary. If we can’t find one in the path, we create a $HOME/.ample directory and downlod it to there